A good friendship is one where people enjoy one another's company, but more importantly both can rely on each other for support and honesty. I think people often refer to others as friends when they are merely good acquaintances. We all have many good acquaintances or 'friends', but only a few good friends.

It is the nature of man I suppose, so too is the ability to be benevolent. The path taken depends on what principles one bases their life on.

It depends on the context, but Tel's definition is the more common one. It doesn't always take on an accusatory tone, it may be said in a jokingly. Domasia is also correct, and this phrases may be used to coax an opinion from someone who is under someone else's influence /control.

Rather may also be used to correct oneself. For example 'I have an appointment with the doctor, or rather, the dentist'

In one sense they are the same. For example 'that was rather good' and 'that was quite good' are similar. Rather may also mean instead of, for example 'I'd rather do this'

You'll absorb the rules naturally as a result of more exposure. I'd say don't bog yourself down with these details, but that's just me. Good luck with your studies.